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The Xindi weapon is inside a vortex with a Xindi-Reptilian starship. Aboard the vessel, CommanderDolim stands with two other Xindi-Reptilian officers, one of whom joins Dolim in imagining how the Xindi would have benefited if the Guardians had made the Reptilians the dominant Xindispecies before their civil wars. Dolim remarks that, thanks to the fact that the Guardians have finally come to their senses, the Reptilians will take their place at the head of a new Xindi empire once Earth is destroyed. They toast to their success by devouring live mice whole.

Aboard Degra's ship, the Xindi-Primate councilor informs CaptainArcher that the weapon is almost three hours ahead of them but notes that they are closing the gap. Malcolm Reed states that their vessel may be faster but is not well-armed and asks how many ships are escorting the weapon, something they do not know. Archer concludes that the only way to destroy the weapon is from the inside, but all of Degra's schematics are encrypted, making it impossible to destroy the weapon. Archer decides that they need Hoshi Sato to help them and, despite Reed's initial objections that she is too weak, he eventually agrees.

In engineering aboard the Enterprise, Trip Tucker reports to T'Pol that the main power grid has been realigned to increase the deflector pulse but it will fry almost every system on board. T'Pol orders him to be prepared to initiate the pulse in two hours but Tucker repeats that, if they do, it will almost certainly destroy the ship. T'Pol gives the order again but Tucker states that the captain told the Xindi they would try to destroy the Spheres and did not say anything about destroying the ship in the process. T'Pol asks Tucker if he realizes what will happen if Earth is destroyed and states that, without Humanity, no one will combat the Sphere-Builders and the Delphic Expanse will continue to grow and will encompass many systems, including Vulcan. She states that Earth is no longer the only world in jeopardy.

In sickbay, Phlox tells T'Pol that the space around the Sphere is being transformed, not unlike the disturbance where the ship found the trans-dimensional being. T'Pol notes that, if they are to disable the Spheres, they will need to get within one kilometer of the surface of Sphere 41, but Phlox points out that if they enter the disturbance, the crew will be dead within minutes. He says that he can synthesize a neuroleptic compound which could keep the crew conscious for about twelve minutes, but suggests that they find a way to shorten the plan to destroy the spheres.

Archer encourages Sato to ignore her self doubts

Aboard Degra's ship, Archer asks Sato if she's had any luck decrypting the schematics. She responds that she isn't feeling very well. She asks for Phlox to come and see her but the Captain reminds her that Phlox isn't there and tells her that she has a job to do. Sato becomes emotional and starts to blame herself for giving the Reptilians the third launch code for the weapon. When Archer says that she had no choice, she blurts out that she should have fought harder to jump off a platform while she was in the weapon. Archer tells her that everything hinges on her decrypting the schematics for the weapon and she returns to work.

On board the weapon, Dolim is told that when they exit the vortex, they will need to be two million kilometers from Earth to allow the firing sequence to start.

In engineering, Tucker tells Mayweather that he has found a way to destroy the sphere without tearing the ship apart but they will need to take power from the impulse engines and travel on thrusters when they reach the anomaly. Mayweather notes that it would be hard with the time limit but Tucker encourages him.

Reed tells Archer that they will not be able to transport directly onto the weapon's control platform due to deflector shielding. Despite Reed's objections, Archer decides to take Sato with him to the weapon because she has been on the weapon before. When asked what will happen if they cannot escape in time, Archer announces that he will give everyone plenty of time to get to the beam out point. Reed asks what Archer intends to do and receives the reply that Archer has no intention of dying on the weapon.

Archer is shown how he will help found the Federation

As he exits the room, Archer finds himself on a balcony overlooking a large hall. Daniels is there and tells him that it is a very important day. Daniels points out a man in a blue jacket, saying that it is Archer a little more than seven years in the future. He reveals that the elder Archer is about to make history, and that he must not risk his life or the United Federation of Planets may never come to be.

Enterprise drops out of warp as it arrives at Sphere 41. Mayweather states that the anomaly is growing and it is one hundred thousand kilometers larger than the first time they encountered it. Phlox informs the bridge crew that he has enhanced the neuroleptic compound as much as he can and that they should stay in the disturbance no more than fifteen minutes. The compound is released and the Enterprise makes its final approach toward Sphere 41.

Back on Degra's ship, Archer tells Sato that they need to disable the reactor at a specific point during the inversion sequence but he does not know the sequence and if this is not done correctly, the internal safeguards will kick in and it will be impossible to overload. Sato tells him that she has the sequence but decrypting it is another problem.

One of the Xindi tells Archer that they have gotten close enough to isolate the weapon's signature. Archer is informed that the Insectoid ship is no longer with Dolim's fleet and that the weapon is being escorted by a single craft, Dolim's ship.

On that vessel, one of Dolim's crew informs him that Degra's ship is less than twenty minutes behind them. Dolim instructs the weapon crew to prepare to initiate the firing sequence as soon as they exit the vortex. It is then reported that there are no Earth vessels in the vicinity and only one orbital station nearby. Much to the Reptilian's delight, the station is unarmed. When Earth is shown on the viewscreen, Dolim comments that the Aquatics would feel at home here, due to the large amount of water present.

Enterprise enters the disturbance surrounding Sphere 41.

Meanwhile, Enterprise has entered the disturbance and Phlox starts the countdown. Mayweather states that he has the sphere on sensors and that it is only twenty thousand kilometers away. T'Pol instructs the crew to use thrusters as soon as they are in visual range. Tucker informs T'Pol that the deflector is standing by and, as he places his hand on the console, he notices that his skin is slowly starting to show the effects of being in the disturbance.

Back by the Weapon, Dolim's vessel exits the portal only 800,000 kilometers ahead, on a direct course for Earth. Just as Archer instructs Reed's team to prepare to beam to the weapon, one of the Xindi at the bridge console notes that Dolim's ship is changing course for a space station. When it comes on screen, Archer identifies it as Yosemite 3, a research station having at least thirty to forty civilians on board. Archer instructs the crew to hail them on the frequency provided, only to be told that they can't get anything through due to the weapon's disruption wave.

Enterprise reaches the sphere and T'Pol instructs them to drop to two thousand meters. Tucker tells Phlox that something is happening to his skin and Mayweather also admits to seeing the same on his own. Phlox responds and informs them that it was expected, that they shouldn't scratch it and that there is only eleven minutes remaining.

Meanwhile, Dolim quotes the Guardian's orders that, once Earth is destroyed, they are to destroy all remaining Humancolonies. The ship begins to fire their weapon, and Yosemite 3 is destroyed.

T'Pol gives Tucker the firing coordinates and the deflector pulse is fired at the sphere. Phlox informs them that there is less than ten minutes to go. In engineering, as the crew continue to check the systems, three Sphere-Builders appear out of thin air and begin to attack with balls of charged particles launched from their palms.

The Sphere-Builders begin to use their trans-dimensional abilities to disrupt Enterprise's power systems in hopes of shutting down the deflector pulse. The power drain is immediately felt on the bridge. In response, T'Pol hails engineering and Tucker states he is losing power for the pulse. Phlox points out that there are nine alien lifeforms, likely the trans-dimensional beings. The environment has been altered enough to sustain their presence.

As Dolim prepares to intercept Degra's ship, calling them pathetic due to their weaker weapons, the Arboreal informs Archer that the intercepting vessel is arming their torpedoes and that there is another vessel approaching at high warp asking for Archer; it is the Andorian, Commander Shran. Shran tells them that their ship is no match for the Reptilian vessel and that he anticipated that they would need assistance.

On Enterprise, the deflector pulse is disappearing and the MACO weapons are not affecting the Sphere-Builders as the pulses pass right through them. Tucker reports that the Sphere-Builders have to be stopped or the process will take additional time, which they no longer have. CorporalKelly orders his men to reset their weapons to a modulating frequency, as per Phlox' instructions. This has an effect and forces the Sphere-Builders to retreat, as they use their abilities to pass through walls to find a new console, where they continue to disrupt the power systems.

Enterprise destroys Sphere 41

Shran's vessel, the Kumari, proceeds to escort Degra's ship and takes weapons fire from the enemy vessels while they approach the weapon. Deciding to fight back to buy Archer time, Shran fires back, and then declares that he no longer owes Archer – now Archer owes him. Archer and his boarding party then beam over to the weapon, surprising the Reptilians and killing them all. Archer switches some power cells to begin the overload process. At this time, Dolim discovers that the boarding party has left the ship and that the Kumari is attempting to distract him. Aboard the weapon, more Reptilians engage the MACOs, one forcing Sato to lose her data pad. Archer attacks the creature, and Reed forces the Reptilian off the platform into a shaft, to the depths of the vessel.

On Enterprise, Phlox informs the crew that their time is up, and T'Pol orders an evacuation. Tucker intervenes by letting them know that he needs a minute to finish his task. Seconds later, when Phlox repeats that they have no time, he concurs and presses a button. The pulse intensifies and the Sphere begins to collapse. A pulse-like signal is emitted and the next Sphere in the network also starts collapsing. The Sphere-Builders aboard Enterprise scream as they dematerialize back to their home realm, allowing the ship's power to return. The crew then discover that the entire Sphere network has been destroyed.

Meanwhile, Shran discovers that a Reptilian, Dolim, has transported to the weapon. Shran orders all weapons targeted on Dolim's ship's starboard engines, destroying the ship in the process as the shields in that area were knocked out in the battle leaving that particular spot vulnerable.

The Superweapon explodes above Earth

On board the weapon, Archer orders Reed to hand him the charges and return to Degra's ship. Reed argues but Archer overrules him, assuring him that he will be right behind him. Archer set the charges on the reactor and detonates them. He climbs back down the shaft to reset the final switch and start an overload. At this time, he is attacked by Dolim. Losing the fight, Archer attaches a final charge to Dolim's back and sets it off, killing Dolim. Archer runs across the platform as explosions go off around him. High above Earth, the Superweapon explodes in a shower of flames and debris with seconds to spare.

Enterprise is holding position to rendezvous with Degra's ship. T'Pol notes that the long-range sensors are detecting no Spheres, that all spatial anomalies within their scanning range have vanished and that the thermobaric clouds they detected earlier are starting to dissipate. While the crew tries to establish communication with Archer, T'Pol shares her age (65) with Tucker, informing him that some Vulcans believe that this information is intimate.

When the ships finally meet, Reed tells the crew that the weapon has been destroyed, but explains that Archer was not able to beam out in time. Enterprise docks with the Xindi-Aquatic cruiser shortly thereafter and T'Pol is told by the Primate that they will be returned to Earth within a day.

He also notes that the Xindi-Insectoids have been unable to ignore recent events and that the Reptilians will soon also be forced to accept that the Sphere-Builders were just using them for their own end. Finally, he tells her that Archer's sacrifice will not be forgotten and wishes them a safe journey.

In sickbay, Phlox mentions that the animals can sense that they are traveling within another ship and are upset by it. Phlox asks T'pol how is crew morale holding up. T'Pol tells him that losing a captain is not easy for any crew. Phlox agrees and states that they are all going to need time to heal. When T'Pol inquires about the well being of Porthos, Archer's dog, Phlox said he will be fine in time. In an uncharacteristic gesture, T'Pol then comforts and pets Porthos for the loss of his best friend.

When the ships near Earth, Enterprise leaves the Xindi vessel and sets a course for home. Hoshi – despite Phlox's medical objections, insists on taking her station as they head home. Earth is soon within visual range, and the entire bridge crew stares in awe at the planet that they fought so hard for and that some of their shipmates gave their lives to save. Reed states that the captain would have been proud at this moment, as Tucker notes that Earth is the prettiest sight he has ever seen, and more importantly, it's in one piece. However things begin to take a strange turn when Hoshi is unable to raise Starfleet Command despite everyone expecting them to be waiting anxiously for news. Scans show that all the orbital platforms are missing and there is no communication with the Lunar One Colony either, despite all of their attempts. T'Pol sends Tucker and Mayweather in a shuttlepod to San Francisco to find out what is going on and at first everything looks fine. However, Mayweather detects three vessels approaching but, as they try to hail them, they hear metallic noises coming from their hull. Three World War II era airplanes, P-51 Mustangs, are flying toward them and firing at them.

Meanwhile, in a Nazi medical camp, a Nazi officer requests to see a patient. A doctor takes the officer to the patient, a man that turns out to be Archer, badly burned. When the doctor asks if they recognize his uniform, an alien in Nazi uniform steps out of the shadows.

"If they had made us the dominant species before the wars, our homeworld would still exist."
"And our avian brothers would still fill the skies."
"We should be grateful that the Guardians have finally come to their senses. Once Earth is destroyed, the Reptilians will take their rightful place at the head of a new Xindi Empire."

- Commander Dolim and one of his Xindi-Reptilian comrades, as they enjoy a tiny mammalian snack

"Has it occurred to you what's going to happen if Captain Archer fails – if Earth is destroyed?"
"Every day!"
"Good. Then you've already come to the conclusion that, without Humanity, there's no one to combat these sphere builders. Their Expanse will continue to grow, encompassing one system after another, including Vulcan. Your world is no longer the only one in jeopardy."

"Captain Archer destroyed the weapon."
"Where is he? Is he okay?"
"Captain didn't make it, Trip."
"What do you mean, he didn't make it?"
"The weapon exploded before he could transport to Degra's ship."

- Reed and Tucker

"Your captain's sacrifice will not be forgotten."

- The Xindi-Primate Councilor, to T'Pol

"You should be in your quarters."
"With all due respect to Phlox, I wouldn't miss this for the world."

- T'Pol and Hoshi, as the ensign enters the bridge for the final approach to Earth

In a special feature on the Season 4 DVD, Connor Trinneer says he believes that the producers deliberately created an ending so ambiguous that, had the series been canceled, the reaction to it ending that way would've been so negative as to make the network execs miserable – calling it a "wily move" on their part.

Rick Berman has compared this episode to Star Trek: Deep Space Nine's Final Chapter arc. He said it "was kind of like the end of Deep Space Nine, in a way. We had a lot of threads that needed to be tied up. We didn't have as many threads as we did with Deep Space Nine because we had so many characters on that show, and "What You Leave Behind" was also a series finale. But here it was a question of how to end the Xindi arc." [1]